Supported Data Types

  • Expression data
    • Affymetrix 3’-IVT arrays
    • Affymetrix genechip ST 1.0 arrays
    • Agilent single and dual channel arrays
    • Illumina expression arrays
    • GenePix data
    • mAdb Archive data
    • GDS datasets from NCBI/GEO
    • Other data types through general importer
  • RNA Sequencing data

Class comparison for differential expression

  • Univariate tests with the option of random variance model
  • Multivariate permutation tests
  • Significance Analysis of Microarrays(SAM)
  • Lassoed Principal Components

Class prediction

  • Compound covariate predictor; SVM; Bayesian compound covariate; KNN; DLDA; Nearest centroid
  • Adaboost
  • PAM
  • Lasso logistic regression
  • Binary tree prediction

Clustering

  • Interactive heat map viewer
  • Hierarchical clustering
  • Non-negative matrix factorization clustering

2-D and 3-D interactive Scatter-plot

Gene Set Enrichment Analysis with many gene sets

  • BioCarta
  • KEGG
  • CGAP
  • Broad Institute - MSigDB
  • Gene Ontology
  • Protein domain
  • Transcription factor targets
  • MicroRNA targets
  • User defined gene lists

Visualization of Samples

  • 3-D interactive plot

Survival Analysis

  • Survival gene sets analysis
  • Survival risk prediction analysis

KEGG Pathway Graphic Tool

The “Gene color coding for KEGG human disease pathways” utility tool displays a KEGG disease pathway graph with selected genes being color-coded by their expression values or fold changes.